Research workbench
Crystal structure of the ternary complex between human T cell receptor, staphylococcal enterotoxin H and human major histocompatibility complex class II
Analyse Crystal structure of the ternary complex between human T cell receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XN9
- Type
- protein
- Length
- 1,035 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T cell receptor alpha chain C region; T cell receptor beta-1 chain C region; Enterotoxin…
- UniProt
- P01848, P01850, P0A0M0, P01903, P04229, A8CDU0
- Ligands
- NA
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T cell receptor alpha chain C region | protein | 199 | 5% helix, 44% strand | P01848 |
| B | T cell receptor beta-1 chain C region | protein | 242 | 6% helix, 49% strand | P01850 |
| C | Enterotoxin H | protein | 215 | 23% helix, 38% strand | P0A0M0 |
| D | HLA class II histocompatibility antigen, dr alpha chain, | protein | 178 | 14% helix, 47% strand | P01903 |
| E | Major histocompatibility complex class II beta chain | protein | 188 | 19% helix, 45% strand | P04229 |
| F | Hemagglutinin | protein | 13 | 0% helix, 8% strand | A8CDU0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.71 | 0.75 | 87 | GOL |
| 2 | 328 | 0.63 | 0.79 | 34 | empty |
| 3 | 158 | 0.51 | 0.78 | 22 | empty |
| 4 | 183 | 0.49 | 0.76 | 22 | empty |
| 5 | 109 | 0.40 | 0.76 | 29 | empty |
Interfaces
9 interfaces between chains.
- D–E · 2538 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2085 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 695 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 668 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 656 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 2XN9 · Crystal structure of the ternary complex between human T cell receptor, staphylococcal… · the same entry in another collection · chain F against F, TM-score 1.00
- P0A0M0 · AlphaFold monomer V2.0 prediction for enterotoxin type H (P0A0M0) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain D against A, TM-score 0.97
- P01850 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 1 (P01850) · a predicted model of the same protein · chain B against A, TM-score 0.53
- P01848 · AlphaFold monomer V2.0 prediction for T cell receptor alpha chain constant (P01848) · a predicted model of the same protein · chain A against A, TM-score 0.44
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01848
- Every structure of UniProt P01850
- Every structure of UniProt P0A0M0
- Every structure of UniProt P01903
- Every structure of UniProt P04229
- Every structure of UniProt A8CDU0
- Elsewhere: RCSB PDB 2XN9 · PDBe 2XN9 · UniProt P01848 · UniProt P01850 · UniProt P0A0M0 · UniProt P01903 · UniProt P04229 · UniProt A8CDU0
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